[2024-01-24 12:09:04,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:04,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:04,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference
[2024-01-24 12:09:06,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,103] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg139e45e5-eabe-4b6b-b96b-a5954def6b4a/GCF_002240035.1_ASM224003v1_genomic.fna.gz | prodigal -d GCF_002240035.1_ASM224003v1_genomic.fna/cds.fna -a GCF_002240035.1_ASM224003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:13,136] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:13,137] [INFO] Task started: HMMsearch
[2024-01-24 12:09:13,137] [INFO] Running command: hmmsearch --tblout GCF_002240035.1_ASM224003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/reference_markers.hmm GCF_002240035.1_ASM224003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:13,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:13,396] [INFO] Found 6/6 markers.
[2024-01-24 12:09:13,425] [INFO] Query marker FASTA was written to GCF_002240035.1_ASM224003v1_genomic.fna/markers.fasta
[2024-01-24 12:09:13,426] [INFO] Task started: Blastn
[2024-01-24 12:09:13,426] [INFO] Running command: blastn -query GCF_002240035.1_ASM224003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/reference_markers.fasta -out GCF_002240035.1_ASM224003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:14,078] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:14,082] [INFO] Selected 8 target genomes.
[2024-01-24 12:09:14,082] [INFO] Target genome list was writen to GCF_002240035.1_ASM224003v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:14,086] [INFO] Task started: fastANI
[2024-01-24 12:09:14,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg139e45e5-eabe-4b6b-b96b-a5954def6b4a/GCF_002240035.1_ASM224003v1_genomic.fna.gz --refList GCF_002240035.1_ASM224003v1_genomic.fna/target_genomes.txt --output GCF_002240035.1_ASM224003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:19,755] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:19,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:19,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:19,770] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:19,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:19,771] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	100.0	1090	1090	95	conclusive
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	83.2377	778	1090	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_001467745.1	455	455	type	True	83.1616	799	1090	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_900640205.1	455	455	type	True	83.1136	780	1090	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	81.4513	119	1090	95	below_threshold
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	79.7519	473	1090	95	below_threshold
Legionella lansingensis	strain=ATCC 49751	GCA_001467795.1	45067	45067	type	True	78.1979	204	1090	95	below_threshold
Legionella gresilensis	strain=Greoux 11D13	GCA_900639865.1	91823	91823	type	True	76.9847	107	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:19,773] [INFO] DFAST Taxonomy check result was written to GCF_002240035.1_ASM224003v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:19,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:19,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:19,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/checkm_data
[2024-01-24 12:09:19,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:19,812] [INFO] Task started: CheckM
[2024-01-24 12:09:19,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002240035.1_ASM224003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002240035.1_ASM224003v1_genomic.fna/checkm_input GCF_002240035.1_ASM224003v1_genomic.fna/checkm_result
[2024-01-24 12:09:46,661] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:46,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:46,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:46,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:46,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002240035.1_ASM224003v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:46,687] [INFO] Task started: Blastn
[2024-01-24 12:09:46,687] [INFO] Running command: blastn -query GCF_002240035.1_ASM224003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81ffed6-5440-411b-970c-d19fa1a9c13d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002240035.1_ASM224003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:47,696] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:47,700] [INFO] Selected 14 target genomes.
[2024-01-24 12:09:47,700] [INFO] Target genome list was writen to GCF_002240035.1_ASM224003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:47,709] [INFO] Task started: fastANI
[2024-01-24 12:09:47,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg139e45e5-eabe-4b6b-b96b-a5954def6b4a/GCF_002240035.1_ASM224003v1_genomic.fna.gz --refList GCF_002240035.1_ASM224003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002240035.1_ASM224003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:56,163] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:56,177] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:56,177] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002240035.1	s__Tatlockia clemsonensis	100.0	1089	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001467745.1	s__Tatlockia jamestowniensis	83.1769	798	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_000953655.1	s__Tatlockia hackeliae	79.763	472	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	-
GCF_001467025.1	s__Tatlockia brunensis	79.3184	327	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900187355.1	s__Tatlockia lansingensis	78.5594	210	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	-
GCF_900452385.1	s__Tatlockia donaldsonii	78.4626	171	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756815.1	s__Tatlockia massiliensis	78.2933	144	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000621525.1	s__Tatlockia fairfieldensis	78.2847	137	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001468035.1	s__Legionella tucsonensis	78.1131	89	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900640175.1	s__Tatlockia sp900640175	78.0236	154	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900639985.1	s__Legionella rowbothamii	77.856	75	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697725.1	s__Tatlockia sp013697725	77.6897	81	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900639875.1	s__Legionella_A impletisoli	77.5365	58	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003184185.1	s__Legionella qingyii	76.8305	75	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:56,179] [INFO] GTDB search result was written to GCF_002240035.1_ASM224003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:56,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:56,183] [INFO] DFAST_QC result json was written to GCF_002240035.1_ASM224003v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:56,183] [INFO] DFAST_QC completed!
[2024-01-24 12:09:56,183] [INFO] Total running time: 0h0m51s